diff options
Diffstat (limited to 'pkgs/applications/science/chemistry')
11 files changed, 64 insertions, 19 deletions
diff --git a/pkgs/applications/science/chemistry/chemtool/default.nix b/pkgs/applications/science/chemistry/chemtool/default.nix index fe2d658b5a44f..82b1834671619 100644 --- a/pkgs/applications/science/chemistry/chemtool/default.nix +++ b/pkgs/applications/science/chemistry/chemtool/default.nix @@ -5,7 +5,7 @@ , libX11 , gtk2 , fig2dev -, wrapGAppsHook +, wrapGAppsHook3 }: stdenv.mkDerivation rec { @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { sha256 = "hhYaBGE4azNKX/sXzfCUpJGUGIRngnL0V0mBNRTdr8s="; }; - nativeBuildInputs = [ pkg-config wrapGAppsHook ]; + nativeBuildInputs = [ pkg-config wrapGAppsHook3 ]; buildInputs = [ libX11 gtk2 diff --git a/pkgs/applications/science/chemistry/cp2k/default.nix b/pkgs/applications/science/chemistry/cp2k/default.nix index 42bfc6ffe32e3..8a831fe23b742 100644 --- a/pkgs/applications/science/chemistry/cp2k/default.nix +++ b/pkgs/applications/science/chemistry/cp2k/default.nix @@ -64,6 +64,12 @@ stdenv.mkDerivation rec { fetchSubmodules = true; }; + patches = [ + # Remove the build command line from the source. + # This avoids dependencies to .dev inputs + ./remove-compiler-options.patch + ]; + nativeBuildInputs = [ python3 which openssh makeWrapper pkg-config ] ++ lib.optional (gpuBackend == "cuda") cudaPackages.cuda_nvcc; @@ -75,6 +81,7 @@ stdenv.mkDerivation rec { libvori libxc libxsmm + mpi spglib scalapack blas @@ -101,7 +108,7 @@ stdenv.mkDerivation rec { ] ; - propagatedBuildInputs = [ mpi ]; + propagatedBuildInputs = [ (lib.getBin mpi) ]; propagatedUserEnvPkgs = [ mpi ]; makeFlags = [ @@ -149,14 +156,16 @@ stdenv.mkDerivation rec { -D__PLUMED2 -D__HDF5 -D__GSL -D__SIRIUS -D__LIBVDWXC -D__SPFFT -D__SPLA \ ${lib.strings.optionalString (gpuBackend == "cuda") "-D__OFFLOAD_CUDA -D__ACC -D__DBCSR_ACC -D__NO_OFFLOAD_PW"} \ ${lib.strings.optionalString (gpuBackend == "rocm") "-D__OFFLOAD_HIP -D__DBCSR_ACC -D__NO_OFFLOAD_PW"} - CFLAGS = -fopenmp -I${lib.getDev hdf5-fortran}/include -I${lib.getDev gsl}/include + CFLAGS = -fopenmp FCFLAGS = \$(DFLAGS) -O2 -ffree-form -ffree-line-length-none \ -ftree-vectorize -funroll-loops -msse2 \ -std=f2008 \ -fopenmp -ftree-vectorize -funroll-loops \ - -I${lib.getDev libint}/include ${lib.optionalString enableElpa "$(pkg-config --variable=fcflags elpa)"} \ + ${lib.optionalString enableElpa "$(pkg-config --variable=fcflags elpa)"} \ + -I${lib.getDev libint}/include \ -I${lib.getDev sirius}/include/sirius \ - -I${lib.getDev libxc}/include -I${lib.getDev libxsmm}/include \ + -I${lib.getDev libxc}/include \ + -I${lib.getDev libxsmm}/include \ -I${lib.getDev hdf5-fortran}/include \ -fallow-argument-mismatch LIBS = -lfftw3 -lfftw3_threads \ diff --git a/pkgs/applications/science/chemistry/cp2k/remove-compiler-options.patch b/pkgs/applications/science/chemistry/cp2k/remove-compiler-options.patch new file mode 100644 index 0000000000000..e6cf81494aa33 --- /dev/null +++ b/pkgs/applications/science/chemistry/cp2k/remove-compiler-options.patch @@ -0,0 +1,37 @@ +diff --git a/src/start/cp2k.F b/src/start/cp2k.F +index f69146ea3..a195f0620 100644 +--- a/src/start/cp2k.F ++++ b/src/start/cp2k.F +@@ -58,8 +58,7 @@ PROGRAM cp2k + USE input_cp2k, ONLY: create_cp2k_root_section + USE input_section_types, ONLY: section_release,& + section_type +- USE iso_fortran_env, ONLY: compiler_options,& +- compiler_version ++ USE iso_fortran_env, ONLY: compiler_version + USE kinds, ONLY: default_path_length + USE machine, ONLY: default_output_unit + #include "../base/base_uses.f90" +@@ -70,7 +69,6 @@ PROGRAM cp2k + arg_att, command + CHARACTER(LEN=default_path_length), & + DIMENSION(:, :), ALLOCATABLE :: initial_variables, initial_variables_tmp +- CHARACTER(LEN=:), ALLOCATABLE :: compiler_options_string + INTEGER :: output_unit, l, i, var_set_sep, inp_var_idx + INTEGER :: ierr, i_arg + LOGICAL :: check, usage, echo_input, command_line_error +@@ -328,14 +326,6 @@ PROGRAM cp2k + WRITE (output_unit, "(T2,A)") cp2k_version, & + "Source code revision "//TRIM(compile_revision), & + TRIM(cp2k_flags()) +- compiler_options_string = compiler_options() +- WRITE (output_unit, "(T2,A,A)") "compiler: ", compiler_version() +- WRITE (output_unit, "(T2,A)") "compiler options:" +- DO i = 0, (LEN(compiler_options_string) - 1)/68 +- WRITE (output_unit, "(T4,A)") & +- compiler_options_string(i*68 + 1:MIN(LEN(compiler_options_string), (i + 1)*68)) +- END DO +- DEALLOCATE (compiler_options_string) + END IF + END IF + diff --git a/pkgs/applications/science/chemistry/element/default.nix b/pkgs/applications/science/chemistry/element/default.nix index c3c4a0fe582ed..cc80cb058d92c 100644 --- a/pkgs/applications/science/chemistry/element/default.nix +++ b/pkgs/applications/science/chemistry/element/default.nix @@ -14,7 +14,7 @@ buildGoModule rec { vendorHash = "sha256-A4g2rQTaYrA4/0rqldUv7iuibzNINEvx9StUnaN2/Yg="; meta = with lib; { - description = "The periodic table on the command line"; + description = "Periodic table on the command line"; mainProgram = "element"; homepage = "https://github.com/gennaro-tedesco/element"; license = licenses.asl20; diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index a4b1cd943e1bb..c379e432bdeb2 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -16,10 +16,10 @@ stdenv.mkDerivation rec { pname = "gwyddion"; - version = "2.65"; + version = "2.66"; src = fetchurl { url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz"; - sha256 = "sha256-kRX7CoPJY8YkYNode5g0OCyWmL+5sM8puCmk9ZE2nqM="; + sha256 = "sha256-N3vtzSsNjRM6MpaG2p9fkYB/8dR5N/mZEZXx6GN5LVI="; }; nativeBuildInputs = [ pkg-config file ]; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index ee3ab5f1f3a56..cba6a40b59923 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.63"; + version = "16.2.17"; pname = "jmol"; src = let baseVersion = "${lib.versions.major version}.${lib.versions.minor version}"; in fetchurl { url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; - hash = "sha256-zUX3msosz0LNQJuEUbFgT32Hw0Wq4CgW1iHMkvReysU="; + hash = "sha256-1iBLLfaoztbphhrG3NVWH+PVSbCZd+HQqvCYF3H9S/E="; }; patchPhase = '' @@ -52,7 +52,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with lib; { - description = "A Java 3D viewer for chemical structures"; + description = "Java 3D viewer for chemical structures"; mainProgram = "jmol"; homepage = "https://sourceforge.net/projects/jmol"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index 090c252bb82ce..4228e818e4887 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -39,7 +39,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "A chemical modelling, analysis and structure drawing program"; + description = "Chemical modelling, analysis and structure drawing program"; homepage = "https://chemaxon.com/products/marvin"; maintainers = with maintainers; [ fusion809 ]; license = licenses.unfree; diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix index a3a385802aaaa..2e87cf3db51aa 100644 --- a/pkgs/applications/science/chemistry/octopus/default.nix +++ b/pkgs/applications/science/chemistry/octopus/default.nix @@ -30,13 +30,13 @@ assert (blas.isILP64 == arpack.isILP64); stdenv.mkDerivation rec { pname = "octopus"; - version = "14.0"; + version = "14.1"; src = fetchFromGitLab { owner = "octopus-code"; repo = "octopus"; rev = version; - sha256 = "sha256-wQ2I+10ZHLKamW3j6AUtq2KZVm6d29+JxYgwvBKz9DU="; + sha256 = "sha256-8wZR+bYdxJFsUPMWbIGYxRdNzjLgHm+KFLjY7fSN7io="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/chemistry/openmolcas/default.nix b/pkgs/applications/science/chemistry/openmolcas/default.nix index 8ad9794739559..d500e78b24820 100644 --- a/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -43,13 +43,13 @@ let in stdenv.mkDerivation rec { pname = "openmolcas"; - version = "24.02"; + version = "24.06"; src = fetchFromGitLab { owner = "Molcas"; repo = "OpenMolcas"; rev = "v${version}"; - hash = "sha256-4Ek0cnaRfLEbj1Nj31rRp9b2sois4rIFTcpOUq9h2mw="; + hash = "sha256-/y6vEvA1Zf+p7Z0WpcN4P5voLN8MmfbKz1FuthgVQp0="; }; patches = [ diff --git a/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/pkgs/applications/science/chemistry/quantum-espresso/default.nix index 4c44829197724..2c565cb5db9f0 100644 --- a/pkgs/applications/science/chemistry/quantum-espresso/default.nix +++ b/pkgs/applications/science/chemistry/quantum-espresso/default.nix @@ -2,7 +2,6 @@ , stdenv , fetchFromGitLab , fetchFromGitHub -, fetchurl , git , cmake , gnum4 diff --git a/pkgs/applications/science/chemistry/siesta/default.nix b/pkgs/applications/science/chemistry/siesta/default.nix index 02586dea2e297..2ec4d37f73ed2 100644 --- a/pkgs/applications/science/chemistry/siesta/default.nix +++ b/pkgs/applications/science/chemistry/siesta/default.nix @@ -63,7 +63,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A first-principles materials simulation code using DFT"; + description = "First-principles materials simulation code using DFT"; mainProgram = "siesta"; longDescription = '' SIESTA is both a method and its computer program |